Carotenoids, the natural pigments that confer the bright orange color of sea buckthorn berries, are also associated with several health benefits, such as antioxidant activity and skin and eye protection. Due to their lipophilic nature and localization, carotenoids are largely retained in the sea buckthorn pomace (SBP) resulting from juice production. Carotenoids from SBP (70.03 mg/100 g DW), extracted and characterized by HPLC-PDA, contained zeaxanthin (free and esterified) and beta-carotene as major compounds. The SBP carotenoids-enriched sunflower oil was further encapsulated in Ca-alginate hydrogel beads (98.4% encapsulation efficiency) using ionotropic gelation. The hydrogel beads were characterized by confocal laser scanning microscopy and scanning electron microscopy. Fairly good stability (>64%) of the encapsulated carotenoids in the alginate hydrogel beads during storage (30 days, 4 °C and 25 °C) was found, with zeaxanthin esters being the most stable compounds, for all the experimental conditions. The bioaccessibility of the total carotenoids (INFOGEST protocol) was 42.1 ± 4.6% from hydrated, and, respectively, 40.8 ± 4% from dehydrated SBP alginate hydrogel beads. The addition of yogurt to the dehydrated hydrogel beads had a positive effect on the bioaccessibility of free and esterified zeaxanthin, but not on that of the carotenes. In conclusion, SBP is a valuable source of carotenoids which can be protected by encapsulation in alginate hydrogel beads, thus still retaining a good bioaccessibility.